I don't usually like to concern myself with questions like these. It is a complete shot in the dark. You never know what the future holds and there are way too many factors to take into account. That goes for both movies I like and movies I don't like.
I can't comment on TDKR's future. However, I do think to a certain degree (and like I said, there is no way of knowing this for sure until time tells) that TDKR will hurt BB & TDK in the eyes of future generations. Ironically, I have this belief due to, as Shauner stated, the trilogy being seen as a "whole" in the future. I think the whole "epic conclusion to this epic three-act trilogy that was always meant to be a three-act trilogy" thing will bleed into BB and TDK in the future and affect the way newcomers will look at these films.
For example, let's take the ending. TDK's ending blew everyone away back when the film came out. No one was expecting him to quit/get depressed/lose hope/whatever way you want to interpret it after that. People walked out of theatres saying things like "Wow, that ending is amazing and it just shows how much Batman is willing to keep going" and "Wow, it was so impressive how Batman took his grief over Rachel and transformed it into something positive". Future generations will say different things due to having foresight. They'll see the ending and might think "So Batman survives this night, disappears, and then quits that same night/after his energy project" (depending on whatever you believe). They might see Rachel's death and think "Oh, so this is part of why he is so depressed and out-of-the-game at the start of TDKR". Cool little easter eggs like "You and I will do this forever" will have nowhere near the same impact. "I don't think there will come a time when you no longer need Batman" won't have the same impact. The list goes on.
Either that or the trilogy as a whole will become the most conspiracy-theorized film franchise since Star Wars. In a way, that is already happening. There are tons of theories flowing out there over what Lucas originally planned, what he didn't plan, whether or not the prequel trilogy was always a go, whether or not they were going to be different and Lucas just sold out, etc. Everyone has their own little theory of the history behind Star Wars. The old-school fans in particular often make statements such as "You don't know but I do because I was there when Star Wars came out and kept up with news, etc.". I can see the Nolan franchise becoming just that, with the milost's/Joker's/Shikamaru's of today saying the same thing to the younger generations - "You don't know, I know because I was there, Goyer originally said x, Nolan said y, Bale said this about Robin"

. In that sense, I guess this trilogy has a lot more in common with the OT than all of us thought.
Me personally, I am really happy to have seen these films in a time where I wouldn't have foresight or have to be bombarded by so many theories. I think everyone should appreciate that, regardless of what their opinion on TDKR is (and by extension, of the whole franchise).